Evaluation of anti-HIV-1 mutagenic nucleoside analogues

J Biol Chem. 2015 Jan 2;290(1):371-83. doi: 10.1074/jbc.M114.616383. Epub 2014 Nov 14.

Abstract

Because of their high mutation rates, RNA viruses and retroviruses replicate close to the threshold of viability. Their existence as quasi-species has pioneered the concept of "lethal mutagenesis" that prompted us to synthesize pyrimidine nucleoside analogues with antiviral activity in cell culture consistent with an accumulation of deleterious mutations in the HIV-1 genome. However, testing all potentially mutagenic compounds in cell-based assays is tedious and costly. Here, we describe two simple in vitro biophysical/biochemical assays that allow prediction of the mutagenic potential of deoxyribonucleoside analogues. The first assay compares the thermal stabilities of matched and mismatched base pairs in DNA duplexes containing or not the nucleoside analogues as follows. A promising candidate should display a small destabilization of the matched base pair compared with the natural nucleoside and the smallest gap possible between the stabilities of the matched and mismatched base pairs. From this assay, we predicted that two of our compounds, 5-hydroxymethyl-2'-deoxyuridine and 5-hydroxymethyl-2'-deoxycytidine, should be mutagenic. The second in vitro reverse transcription assay assesses DNA synthesis opposite nucleoside analogues inserted into a template strand and subsequent extension of the newly synthesized base pairs. Once again, only 5-hydroxymethyl-2'-deoxyuridine and 5-hydroxymethyl-2'-deoxycytidine are predicted to be efficient mutagens. The predictive potential of our fast and easy first line screens was confirmed by detailed analysis of the mutation spectrum induced by the compounds in cell culture because only compounds 5-hydroxymethyl-2'-deoxyuridine and 5-hydroxymethyl-2'-deoxycytidine were found to increase the mutation frequency by 3.1- and 3.4-fold, respectively.

Keywords: Antiviral Agent; Human Immunodeficiency Virus (HIV); Lethal; Mutagenesis; Nucleoside/Nucleotide Analogue; Reverse Transcription.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-HIV Agents / chemistry*
  • Anti-HIV Agents / metabolism
  • Anti-HIV Agents / pharmacology
  • Base Pair Mismatch
  • Base Pairing
  • Base Sequence
  • Deoxycytidine / analogs & derivatives
  • Deoxycytidine / chemistry
  • Deoxycytidine / metabolism
  • Deoxycytidine / pharmacology
  • Drug Design
  • HIV Reverse Transcriptase / antagonists & inhibitors
  • HIV Reverse Transcriptase / chemistry
  • HIV Reverse Transcriptase / genetics*
  • HIV-1 / drug effects
  • HIV-1 / enzymology
  • HIV-1 / genetics*
  • High-Throughput Screening Assays / economics*
  • Molecular Sequence Data
  • Mutagenesis
  • Mutagens / chemistry*
  • Mutagens / metabolism
  • Mutagens / pharmacology
  • Nucleic Acid Denaturation
  • Predictive Value of Tests
  • Reverse Transcriptase Inhibitors / chemistry*
  • Reverse Transcriptase Inhibitors / metabolism
  • Reverse Transcriptase Inhibitors / pharmacology
  • Reverse Transcription
  • Thermodynamics
  • Thymidine / analogs & derivatives
  • Thymidine / chemistry
  • Thymidine / metabolism
  • Thymidine / pharmacology
  • Time Factors

Substances

  • 5-hydroxymethyl-2'-deoxycytidine
  • Anti-HIV Agents
  • Mutagens
  • Reverse Transcriptase Inhibitors
  • Deoxycytidine
  • 5-hydroxymethyl-2'-deoxyuridine
  • HIV Reverse Transcriptase
  • Thymidine